On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth

Mulkidjanian, Armen Y.; Galperin, Michael Y.

doi:10.1186/1745-6150-4-27

Cited by 85 publications

(90 citation statements)

References 338 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A recent paper in PNAS (1) analyzed the evolution of metalloproteins and confirmed our earlier observation on the abundance of Zn-binding proteins among the most widespread-and evolutionarily oldest-protein folds (2). Because that observation seemed to contradict the extremely low (<10 −12 M) estimates of Zn levels in the primeval anoxic ocean (3), we had suggested that the first cells developed in continental Zn-rich environments (2,4).…”

mentioning

confidence: 52%

“…Because that observation seemed to contradict the extremely low (<10 −12 M) estimates of Zn levels in the primeval anoxic ocean (3), we had suggested that the first cells developed in continental Zn-rich environments (2,4). Specifically, we proposed that hydrothermal precipitates of zinc sulfide (ZnS), similar to those seen at modern deep sea vents, catalyzed abiogenic photosynthesis of organic compounds under the solar light (2,4).…”

mentioning

confidence: 99%

“…This led to the release of Zn ions, yielding a Zn-rich milieu. In the course of evolution, cells have maintained the initial metal homeostasis and preserved high levels of Zn in the cytoplasm (2).…”

mentioning

confidence: 99%

See 2 more Smart Citations

On the abundance of zinc in the evolutionarily old protein domains

Galperin

2010

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

mentioning

confidence: 52%

mentioning

confidence: 99%

See 1 more Smart Citation

On the abundance of zinc in the evolutionarily old protein domains

Galperin

2010

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

“…Recently, Mulkidjanian and Galperin suggested that the Zn-binding proteins and RNA structures found in all of modern life must have been present in the last universal common ancestor (41). Invoking the hypothesized Zn concentrations in the Archean ocean (9), they concluded that the last universal common ancestor must have evolved near metal-rich hydrothermal vents (41).…”

Section: Emergence Of the Akaryotes Metal Homeostasis And Biogeochementioning

confidence: 99%

History of biological metal utilization inferred through phylogenomic analysis of protein structures

Dupont

Butcher

Valas³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

279

248

View full text Add to dashboard Cite

The fundamental chemistry of trace elements dictates the molecular speciation and reactivity both within cells and the environment at large. Using protein structure and comparative genomics, we elucidate several major influences this chemistry has had upon biology. All of life exhibits the same proteome size-dependent scaling for the number of metal-binding proteins within a proteome. This fundamental evolutionary constant shows that the selection of one element occurs at the exclusion of another, with the eschewal of Fe for Zn and Ca being a defining feature of eukaryotic proteomes. Early life lacked both the structures required to control intracellular metal concentrations and the metal-binding proteins that catalyze electron transport and redox transformations. The development of protein structures for metal homeostasis coincided with the emergence of metal-specific structures, which predominantly bound metals abundant in the Archean ocean. Potentially, this promoted the diversification of emerging lineages of Archaea and Bacteria through the establishment of biogeochemical cycles. In contrast, structures binding Cu and Zn evolved much later, providing further evidence that environmental availability influenced the selection of the elements. The late evolving Zn-binding proteins are fundamental to eukaryotic cellular biology, and Zn bioavailability may have been a limiting factor in eukaryotic evolution. The results presented here provide an evolutionary timeline based on genomic characteristics, and key hypotheses can be tested by alternative geochemical methods.Archean-Proterozoic | biogeochemistry | bioinorganic chemistry | evolution | metal homeostasis M etalloproteins contain one or more ions of an inorganic element in their 3D structure and are said to comprise 30% of all proteins (1). Many biological pathways contain at least one metalloenzyme (2) and consequently require Mg, K, Ca, Fe, Mn, and Zn to sustain life (3). Other elements, like Cu, Mo, Ni, Se, and Co, are required by many-though not all-organismal lineages, and the utilization of trace elements varies greatly between species (3). The different elements have a range of affinities for most coordinating environments in the order Mg +2 /Ca +2 < Mn +2 < Fe +2 < Co +2 < Ni +2 < Cu +2 ∼Zn +2 , an equilibrium series known as the Irving-Williams Series (4). This array of outer-sphere chemistry provides significant catalytic diversity, yet has consequences for both biological and environmental chemistry. Within the cell, metals compete for protein binding sites; hence, extensive protein networks involving transporters and metalsensing regulatory proteins are required to maintain the proper subcellular concentrations of each element, and in some cases directly shuttle each metal to its requisite metalloprotein in the proper cellular compartment (1, 5, 6). It has been hypothesized that the establishment of a metal homeostasis system is required for distinct phylotypes of cells to develop (7).Environmentally, for similar fundamental chemical reasons, the...

show abstract

“…The principle of chemistry conservation can be used as an additional major constraint for reconstructing primordial environmental conditions in the absence of reliable geological record. For example, ancient, ubiquitous proteins often use Zn and Mn, but not Fe, as transition metal cofactors; this preference is retained across the three domains of life (12). The abundance of Zn-and Mn-dependent enzymes during the earliest steps of evolution and the later recruitment of Fe has been inferred also from a global phylogenomic reconstruction (13).…”

mentioning

confidence: 99%

Origin of first cells at terrestrial, anoxic geothermal fields

Mulkidjanian

Bychkov²,

Dibrova³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

366

336

View full text Add to dashboard Cite

All cells contain much more potassium, phosphate, and transition metals than modern (or reconstructed primeval) oceans, lakes, or rivers. Cells maintain ion gradients by using sophisticated, energydependent membrane enzymes (membrane pumps) that are embedded in elaborate ion-tight membranes. The first cells could possess neither ion-tight membranes nor membrane pumps, so the concentrations of small inorganic molecules and ions within protocells and in their environment would equilibrate. Hence, the ion composition of modern cells might reflect the inorganic ion composition of the habitats of protocells. We attempted to reconstruct the "hatcheries" of the first cells by combining geochemical analysis with phylogenomic scrutiny of the inorganic ion requirements of universal components of modern cells. These ubiquitous, and by inference primordial, proteins and functional systems show affinity to and functional requirement for K + , Zn 2+ , Mn 2+, and phosphate. Thus, protocells must have evolved in habitats with a high K + /Na + ratio and relatively high concentrations of Zn, Mn, and phosphorous compounds. Geochemical reconstruction shows that the ionic composition conducive to the origin of cells could not have existed in marine settings but is compatible with emissions of vapor-dominated zones of inland geothermal systems. Under the anoxic, CO 2 -dominated primordial atmosphere, the chemistry of basins at geothermal fields would resemble the internal milieu of modern cells. The precellular stages of evolution might have transpired in shallow ponds of condensed and cooled geothermal vapor that were lined with porous silicate minerals mixed with metal sulfides and enriched in K + , Zn 2+, and phosphorous compounds.

show abstract

On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth

Cited by 85 publications

References 338 publications

On the abundance of zinc in the evolutionarily old protein domains

On the abundance of zinc in the evolutionarily old protein domains

History of biological metal utilization inferred through phylogenomic analysis of protein structures

Origin of first cells at terrestrial, anoxic geothermal fields

Contact Info

Product

Resources

About